Analysis of the algorithm: From rankings to backup genes.

Ranking section

Table 1. Performance summary for every kernel and net before integration.

Net Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
biological_process ct 0.0843958712811172 0.117182756527019 0.000337343197135966 0.000708617548572519 0.127833519137867
biological_process el 0.0127427184466019 0.0254854368932039 0.00402508690707786 0.0112218193990885 0.00521045347227876
biological_process ka 0.134775349119611 0.170006071645416 0.00045779032189103 0.000789437047867043 0.173853989813243
biological_process rf 0.0831663630843959 0.117805100182149 0.000356609522935531 0.000721665987087651 0.12778603268945
cellular_component ct 0.0697815533980582 0.0989077669902913 0.000433386056000642 0.00104318726237029 0.0964673913043478
cellular_component el 0.0260764099454215 0.0436779866585809 0.0238847873665587 0.0425655399882364 0.00196536884551523
cellular_component ka 0.070995145631068 0.0989077669902913 0.000449575353299178 0.00114773391515818 0.0987569060773481
cellular_component rf 0.0582372572815534 0.087378640776699 0.000300602559654239 0.0006481449644122 0.10048231511254
disease ct 0.346558219178082 0.410291095890411 0.00177350953889026 0.00222690724566255 0.224313725490196
disease el 0.177397260273973 0.217808219178082 0.00621742159430739 0.00808377977956052 0.0450339296730413
disease ka 0.28972602739726 0.358921232876712 0.000418001442013708 0.000662596172275005 0.3674228337672
disease rf 0.344520547945205 0.413013698630137 0.00178274268573532 0.00225071264074084 0.226482213438735
gene_PS ct 0.21379980563654 0.295432458697765 0.0014734099393209 0.00199233626293962 0.191381065490329
gene_PS el 0.229571984435798 0.321035992217899 0.000668434471343864 0.00100647651076217 0.292846855496879
gene_PS ka 0.372568093385214 0.443579766536965 0.00094429108615953 0.00136047680827306 0.331782945736434
gene_PS rf 0.329766536964981 0.417339494163424 0.00110905186292657 0.00155536526993464 0.302395209580838
gene_TF ct 0.0285714285714286 0.114285714285714 0.0229543094496366 0.0987839536536044 0.0051907604464054
gene_TF el 0 0.0214285714285714 0.00276520741105099 0.0350122970978849 0.00472813238770686
gene_TF ka 0.0428571428571429 0.128571428571429 0.044582991747281 1 0.00450704225352113
gene_TF rf 0.1 0.214285714285714 0.0625233644859813 0.196682242990654 0.00622259934945552
gene_hgncGroup ct 0.0883652430044183 0.120784241531664 0.00111448721402568 0.00189872854924986 0.0835975785528971
gene_hgncGroup el 0.114204126750184 0.156963890935888 0.000864105762922642 0.0013470169702303 0.125613346418057
gene_hgncGroup ka 0.110537951363301 0.148120854826824 0.000418245302953257 0.000924803120562144 0.155866900175131
gene_hgncGroup rf 0.0972733971997052 0.133382461311717 0.000725190160902339 0.00132070270612072 0.111072783718524
genetic_interaction_effect_bicor ct 0.0323785803237858 0.0523038605230386 0.000583144838823794 0.00186037380873256 0.0431519699812383
genetic_interaction_effect_bicor el 0.00186799501867995 0.00933997509339975 0.000125947385911688 0.002000552083445 0.00932159502848265
genetic_interaction_effect_bicor ka 0.0330012453300125 0.0529265255292653 0.000427154465443864 0.00106022801582282 0.0520361990950226
genetic_interaction_effect_bicor rf 0.0323785803237858 0.0523038605230386 0.000585315652369671 0.0017892729650633 0.0431789737171464
molecular_function ct 0.0557256582976118 0.0826852418860992 0.000410505132369438 0.00112406119375737 0.0845173041894353
molecular_function el 0.00489596083231334 0.0140758873929009 0.00462627128705035 0.013561147093353 0.00227305014916892
molecular_function ka 0.0648958971218616 0.0930802204531537 0.000614649651281694 0.00133083072942224 0.0818494220556076
molecular_function rf 0.0557256582976118 0.0820575627679118 0.000357173761862701 0.0011439400894669 0.0857771260997068
pathway ct 0.13323124042879 0.203675344563553 0.00138046479364146 0.00257948169460714 0.138707765263782
pathway el 0.165644171779141 0.237730061349693 0.000486892889544211 0.00104742411065911 0.243816254416961
pathway ka 0.193251533742331 0.273006134969325 0.000666247503387193 0.00177872450208699 0.250587314017228
pathway rf 0.159509202453988 0.23159509202454 0.00073980040765907 0.00143018112295893 0.203519510328998
phenotype ct 0.212305611899932 0.271129141311697 0.000628617000967606 0.000906350340089529 0.251090970124203
phenotype el 0.0297128378378379 0.0506756756756757 0.00116914208298939 0.00267455283121653 0.0283687943262411
phenotype ka 0.225135226504395 0.290060851926978 0.000407976596654473 0.00059830124730221 0.308575803981623
phenotype rf 0.212288708586883 0.271129141311697 0.000615518335455486 0.000899808441309355 0.250924991590986
protein_interaction ct 0.259615384615385 0.305288461538462 0.000934940345952621 0.00128462667803673 0.228639618138425
protein_interaction el 0.260802283653846 0.3197265625 0.00068313464164908 0.000946886152328165 0.280022446689113
protein_interaction ka 0.26035778713169 0.307276007215875 0.000632959341874322 0.000965050001706543 0.272212790039615
protein_interaction rf 0.252403846153846 0.300495793269231 0.000797886781680821 0.00106634421608361 0.244357976653696

Table 2. Performance summary for every kernel after integration

Integration Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
integration_mean_by_presence ct 0.173031026252983 0.220763723150358 0.000637454143310874 0.000889986519979975 0.203863298662704
integration_mean_by_presence el 0.365373134328358 0.422089552238806 0.000558050999382935 0.000805838569148928 0.377771540836374
integration_mean_by_presence ka 0.324164179104478 0.372537313432836 0.000296465394887956 0.000511424926637029 0.39986399183951
integration_mean_by_presence rf 0.256716417910448 0.307462686567164 0.000546266246672955 0.000800709188208784 0.286556603773585
mean ct 0.24582338902148 0.294152744630072 0.000902245746715143 0.00136495461521416 0.225900681596884
mean el 0.337313432835821 0.405985074626866 0.000587814232288119 0.000814032755200808 0.367034834324554
mean ka 0.35044776119403 0.426268656716418 0.000413928218417247 0.000662754487823619 0.424922118380062
mean rf 0.285955223880597 0.343880597014925 0.000737092041098652 0.00110847204461741 0.283033620015637

Backup Pairs Coverage By Layer Non integrated

Backup Pairs Coverage By Layer Integrated

Distribution of ranks in dataset by non integrated kernels

Distribution of ranks in dataset by Integrated kernels

ROC-AUCs for Non-integrated kernel and layer

ROC-AUCS for integrated kernels

CDF plots of non integrated kernels

ROC plots of non integrated kernels

ROC plots of integrated kernels

CDF plots of integrated kernels